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bioformats

Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.

bioimagexd-svn-import-from-sourceforge

chalkie666.github.io

Chalkie.org.uk website

colocalisation_analysis

Coloc 2 is Fiji's plugin for colocalization analysis. It implements and performs the pixel intensity correlation over space methods of Pearson, Manders, Costes, Li and more, for scatterplots, analysis, automatic thresholding and statistical significance testing.

cuda_simrecon

Image reconstruction for structured-illumination microscopy implemented in CUDA

cudadecon

cudasirecon

3D Structured illumination microscopy (3D-SIM) reconstruction software

deltavisionscripts

a home for miscellaneous scripts for experiment .exp files and other tools used for work arounds or other clever tricks on DeltaVision microscope systems.

empy

Electromagnetic Python

fiji

A "batteries-included" distribution of ImageJ :battery:

flowdec

TensorFlow Deconvolution for Microscopy Data

imagej.github.io

GitHub Pages for ImageJ

imagejmacros

imageJ 1 macros

oilcalc

python script etc. for calculating refractive index of immersion oils to compensate sample induced spherical aberration

opensim

OpenSIM matlab code

pycudadecon

Python wrapper for cudaDecon - 3D deconvolution for microscopy

rlm_rlog_data_extractor

rlm_rlog_data_extractor for imaris license server log files